3O2X

MMP-13 in complex with selective tetrazole core inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

MMP-13 in complex with selective tetrazole core inhibitor

Barta, T.E.Becker, D.P.Bedell, L.J.Hockerman, S.L.Kiefer, J.R.Li, M.H.Villamill, C.I.Rico, J.G.Mcdonald, J.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagenase 3
A, B, C, D
164Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
PHAROS:  P45452
GTEx:  ENSG00000137745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3O2
Query on 3O2

Download Ideal Coordinates CCD File 
CA [auth D],
E [auth A],
N [auth B],
W [auth C]
N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide
C26 H31 F3 N6 O7 S
MTRATHZFTCSGDT-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
M [auth A],
V [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth C]
HA [auth D]
IA [auth D]
J [auth A]
K [auth A]
BA [auth C],
HA [auth D],
IA [auth D],
J [auth A],
K [auth A],
L [auth A],
S [auth B],
T [auth B],
U [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
F [auth A]
G [auth A]
O [auth B]
DA [auth D],
EA [auth D],
F [auth A],
G [auth A],
O [auth B],
P [auth B],
X [auth C],
Y [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
FA [auth D]
GA [auth D]
H [auth A]
I [auth A]
AA [auth C],
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3O2 BindingDB:  3O2X Ki: 0.13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.864α = 90
b = 95.257β = 90
c = 120.076γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection, Database references, Derived calculations